[2024-01-24 13:36:32,395] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:32,396] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:32,396] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9ff5228-9b53-4c1a-beb4-84d31f41964e/dqc_reference
[2024-01-24 13:36:33,693] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:33,694] [INFO] Task started: Prodigal
[2024-01-24 13:36:33,694] [INFO] Running command: gunzip -c /var/lib/cwl/stg3794906d-d82b-48b9-bd8f-553e54f4eab5/GCF_000228725.2_ASM22872v3_genomic.fna.gz | prodigal -d GCF_000228725.2_ASM22872v3_genomic.fna/cds.fna -a GCF_000228725.2_ASM22872v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:50,161] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:50,162] [INFO] Task started: HMMsearch
[2024-01-24 13:36:50,162] [INFO] Running command: hmmsearch --tblout GCF_000228725.2_ASM22872v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9ff5228-9b53-4c1a-beb4-84d31f41964e/dqc_reference/reference_markers.hmm GCF_000228725.2_ASM22872v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:50,469] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:50,470] [INFO] Found 6/6 markers.
[2024-01-24 13:36:50,514] [INFO] Query marker FASTA was written to GCF_000228725.2_ASM22872v3_genomic.fna/markers.fasta
[2024-01-24 13:36:50,514] [INFO] Task started: Blastn
[2024-01-24 13:36:50,514] [INFO] Running command: blastn -query GCF_000228725.2_ASM22872v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9ff5228-9b53-4c1a-beb4-84d31f41964e/dqc_reference/reference_markers.fasta -out GCF_000228725.2_ASM22872v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:51,261] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:51,264] [INFO] Selected 22 target genomes.
[2024-01-24 13:36:51,264] [INFO] Target genome list was writen to GCF_000228725.2_ASM22872v3_genomic.fna/target_genomes.txt
[2024-01-24 13:36:51,303] [INFO] Task started: fastANI
[2024-01-24 13:36:51,303] [INFO] Running command: fastANI --query /var/lib/cwl/stg3794906d-d82b-48b9-bd8f-553e54f4eab5/GCF_000228725.2_ASM22872v3_genomic.fna.gz --refList GCF_000228725.2_ASM22872v3_genomic.fna/target_genomes.txt --output GCF_000228725.2_ASM22872v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:06,811] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:06,812] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9ff5228-9b53-4c1a-beb4-84d31f41964e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:06,812] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9ff5228-9b53-4c1a-beb4-84d31f41964e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:06,829] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:37:06,829] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:37:06,829] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Rhabdochromatium marinum	strain=DSM 5261	GCA_016583795.1	48729	48729	type	True	79.3029	623	1776	95	below_threshold
Halochromatium roseum	strain=DSM 18859	GCA_016653315.1	391920	391920	type	True	77.9867	287	1776	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	77.771	294	1776	95	below_threshold
Halochromatium glycolicum	strain=DSM 11080	GCA_016584085.1	85075	85075	type	True	77.7654	273	1776	95	below_threshold
Halochromatium salexigens	strain=DSM 4395	GCA_016653295.1	49447	49447	type	True	77.7139	309	1776	95	below_threshold
Thiohalocapsa halophila	strain=DSM 6210	GCA_016583825.1	69359	69359	type	True	77.5287	300	1776	95	below_threshold
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	77.4907	250	1776	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	77.2837	264	1776	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	77.2656	275	1776	95	below_threshold
Thioflavicoccus mobilis	strain=8321	GCA_000327045.1	80679	80679	type	True	77.2615	187	1776	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	77.2412	261	1776	95	below_threshold
Thiocystis violascens	strain=DSM 198	GCA_000227745.3	73141	73141	type	True	77.2118	248	1776	95	below_threshold
Thiocystis minor	strain=DSM 178	GCA_016653465.1	61597	61597	type	True	77.2	256	1776	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	76.1934	76	1776	95	below_threshold
Halomonas elongata	strain=type strain: DSM 2581	GCA_000196875.2	2746	2746	type	True	76.1614	61	1776	95	below_threshold
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	76.028	90	1776	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	75.9955	75	1776	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	75.9547	77	1776	95	below_threshold
Thermithiobacillus tepidarius	strain=DSM 3134	GCA_000423825.1	929	929	type	True	75.952	93	1776	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	75.9329	81	1776	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	75.8905	88	1776	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	75.8171	90	1776	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:06,831] [INFO] DFAST Taxonomy check result was written to GCF_000228725.2_ASM22872v3_genomic.fna/tc_result.tsv
[2024-01-24 13:37:06,832] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:06,832] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:06,833] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9ff5228-9b53-4c1a-beb4-84d31f41964e/dqc_reference/checkm_data
[2024-01-24 13:37:06,834] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:06,890] [INFO] Task started: CheckM
[2024-01-24 13:37:06,890] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000228725.2_ASM22872v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000228725.2_ASM22872v3_genomic.fna/checkm_input GCF_000228725.2_ASM22872v3_genomic.fna/checkm_result
[2024-01-24 13:37:58,185] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:58,187] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:58,209] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:58,210] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:58,210] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000228725.2_ASM22872v3_genomic.fna/markers.fasta)
[2024-01-24 13:37:58,211] [INFO] Task started: Blastn
[2024-01-24 13:37:58,211] [INFO] Running command: blastn -query GCF_000228725.2_ASM22872v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9ff5228-9b53-4c1a-beb4-84d31f41964e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000228725.2_ASM22872v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:59,408] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:59,412] [INFO] Selected 19 target genomes.
[2024-01-24 13:37:59,413] [INFO] Target genome list was writen to GCF_000228725.2_ASM22872v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:59,440] [INFO] Task started: fastANI
[2024-01-24 13:37:59,440] [INFO] Running command: fastANI --query /var/lib/cwl/stg3794906d-d82b-48b9-bd8f-553e54f4eab5/GCF_000228725.2_ASM22872v3_genomic.fna.gz --refList GCF_000228725.2_ASM22872v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000228725.2_ASM22872v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:15,620] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:15,639] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:15,639] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000228725.2	s__Thiorhodovibrio sp000228725	100.0	1775	1776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiorhodovibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016653415.1	s__Thiorhodovibrio winogradskyi	85.2022	949	1776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiorhodovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583795.1	s__Rhabdochromatium marinum	79.312	621	1776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Rhabdochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008632335.1	s__Thiohalocapsa marina	77.756	297	1776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiohalocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003562815.1	s__Halochromatium sp003562815	77.7358	255	1776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	99.58	99.39	0.91	0.88	4	-
GCF_016653295.1	s__Halochromatium salexigens	77.6957	311	1776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583825.1	s__Thiohalocapsa halophila	77.5193	301	1776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiohalocapsa	95.0	95.31	95.31	0.87	0.87	2	-
GCA_009908845.1	s__Halochromatium sp009908845	77.4522	221	1776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938795.1	s__Marichromatium sp016938795	77.2259	203	1776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001469165.1	s__Thiohalocapsa sp001469165	77.2035	320	1776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiohalocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693535.1	s__Halochromatium sp007693535	76.7512	228	1776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Halochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013426805.1	s__Lamprocystis sp013426805	76.6261	208	1776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Lamprocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379525.1	s__Lamprocystis purpurea	76.3885	244	1776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Lamprocystis	95.0	99.73	99.73	0.99	0.99	2	-
GCA_903897335.1	s__Chromatium sp903897335	76.1171	119	1776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Chromatium	95.0	99.90	99.90	0.95	0.95	2	-
GCF_001545155.1	s__Halomonas chromatireducens	76.0661	60	1776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016218375.1	s__JAHJQQ01 sp016218375	76.0476	61	1776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__JAHJQQ01;f__JAHJQQ01;g__JAHJQQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019061305.1	s__Marinobacterium sp019061305	75.7915	51	1776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:15,641] [INFO] GTDB search result was written to GCF_000228725.2_ASM22872v3_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:15,641] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:15,646] [INFO] DFAST_QC result json was written to GCF_000228725.2_ASM22872v3_genomic.fna/dqc_result.json
[2024-01-24 13:38:15,646] [INFO] DFAST_QC completed!
[2024-01-24 13:38:15,646] [INFO] Total running time: 0h1m43s